Mr Collins conceded that in hindsight "we need even additional ... spare drivers", while Labor and the unions blamed the widespread disruption on an overhaul of the rail timetable in November.

Sydney Trains chief executive Howard Collins says the railway is "flat out" training more train drivers and guards, as the city endured a second day of major delays on its stretched rail network.

A lack of staff, plus damage to rail infrastructure caused by lightning strikes, resulted in major delays to services on multiple rail lines on Tuesday, a day after at least 18 services had to be cancelled due to insufficient numbers of drivers and guards.

Passengers faced long queues and overcrowded platforms at Sydney's main stations including Wynyard, Town Hall and Central during the evening peak on Tuesday as the impact of the delays rippled across the rail network. Passengers have been temporarily stopped from entering some platforms to avoid dangerous overcrowding.

Commuters were advised to delay any non-essential travel and use local bus routes where possible due to the "extended delays continuing throughout the evening".

It is the second time in a month that the network has faced severe levels of disruption during the evening peak.

But with demand for public transport surging, Mr Collins said deferring the timetable changes in November would have resulted in people experiencing greater crowding and delays.

"The choice we had was trying to do a service with not enough capacity, people bitterly complaining about crowding on several lines [and] about not being able to get on trains, particularly on weekends," he said.

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"[But] we have seen an improved service, particularly at weekends [from the new timetable]. It is true to say that when big incidents occur, the service takes longer to recover."

Leaked internal documents have revealed that the new timetable has reduced the flexibility in the system to recover from delays caused by major incidents.

Decades-old S-set trains are being pressed into service more often to allow Sydney Trains to put on the 1500 extra weekly services rolled out as part of the timetable changes. It means passengers face uncomfortable journeys on hot summer days because those trains are not airconditioned.

Mr Collins admitted the "awful S-sets" were "not acceptable", but he said they would begin to be replaced from June with 24 new Waratah trains, the first of which is due to be shipped from China next month.

"By next summer, all those S-sets, I want to make sure are gone," he said.

On Tuesday, the T1 North Shore, Northern and Western line suffered "major delays" due to both a lack of staff and lightning strikes damaging signalling equipment at Gordon in Sydney's north.

The T2 Inner West and Leppington, the T3 Bankstown and the T8 Airport and South lines also had major disruptions because of the lack of staff and the need for urgent repairs to signal equipment at Yagoona in the city's west.

The lack of drivers also forced Sydney Trains to use buses instead of trains on the T6 Carlingford and T7 Olympic Park lines for periods of the day.

About 70 train crew called in sick on Tuesday. In all, Sydney Trains has about 3000 train crew.

Labor leader Luke Foley said the new rail timetable was "not worth the paper it's written on" because the train services were "shambolic right now".

"At the moment you have to say our public train system is shambolic in its delivery. If they're this bad now, what will they be in a month's time when everyone is back at work," he said.

But Transport Minister Andrew Constance said Labor was "conveniently ignoring" the new metro and light rail lines under construction, new ferries and thousands of extra buses "making journeys easier".

"In total, $41.5 billion of transport infrastructure is being delivered, after Labor did nothing for 16 years," he said.

The prospect of thousands of rail workers taking industrial action also looms over Sydney Trains and NSW Trains over the coming months.

A ballot of rail workers on whether to take protected industrial action during the negotiating period is due to be released later this week.

The unions representing rail staff have been pushing for a pay rise of 6 per cent a year over the term of a new agreement, which is significantly higher than the 2.5 per cent annual increase Sydney Trains has put on the table.

Mr Collins said most commuters would be "aghast" at what the unions were seeking, but Rail Tram and Bus Union state secretary Alex Claassens said the claim for a 6 per cent rise was a "starting point" in the negotiations which began six months ago.

Mr Claassens said there had been an increase of about 2 per cent in the number of drivers and guards who called in sick over the past two days.

"We have always said we needed extra services. The problem is that ... there are no spare trains in the system and there are no spare drivers and guards," he said.

Sydney's rail network will face one of its biggest tests late this year when the Epping-to-Chatswood line in the city's north is closed for seven months to allow for it to be converted to carry single-deck metro trains.